Saturday, October 10, 2015

Scale bar for cophylo plotting

I just added the option to the phytools function cophylo (for co-phylogenetic plotting) to show separate scale bars for the right & left plotted trees.

Here's a quick demo of how it works:

library(devtools)
install_github("liamrevell/phytools",quiet=TRUE)
## Installing 1 packages: expm
## package 'expm' successfully unpacked and MD5 sums checked
library(phytools)
## Loading required package: ape
## Loading required package: maps
## 
##  # ATTENTION: maps v3.0 has an updated 'world' map.        #
##  # Many country borders and names have changed since 1990. #
##  # Type '?world' or 'news(package="maps")'. See README_v3. #

First, simulate some trees:

t1<-rtree(n=26,tip.label=LETTERS)
t2<-rtree(n=26,tip.label=LETTERS)

The basic plots, no scale bar, look as follows:

obj<-cophylo(t1,t2)
## Rotating nodes to optimize matching...
## Done.
plot(obj)

plot of chunk unnamed-chunk-3

Now let's try with the same scale bar, 2.5 units in length, on either side:

plot(obj,scale.bar=rep(2.5,2))

plot of chunk unnamed-chunk-4

We can use different scale bars:

plot(obj,scale.bar=c(2.5,3.5))

plot of chunk unnamed-chunk-5

And, finally, if we set either to zero it turns off:

plot(obj,scale.bar=c(3,0))

plot of chunk unnamed-chunk-6

Note that the latter plot might be misinterpreted as a single scale bar for both the right & left plotted trees - but this would be wrong (unless the two trees happen to have exactly the same total height) as the trees are always rescaled internally before plotting in this function!

That's it!

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